There are two basic areas where you need to fine-tune a commercial turnout, and in some cases there's little you can do to really fix them. In other words, the real solution is going with a jig-built turnout using something like the Fast Tracks jigs or the Central Valley turnout kits.
But let's assume you want to do what you can to tune a commercial turnout. There are two areas: mechanical improvements and electrical improvements.
MECHANICAL IMPROVEMENTS
I explain some of the mechanical issues here with illustrations. The two key issues are the frog area and the points area. You need to make sure the points are sharp -- if they are not, take a needle file to them and sharpen the top edge of the points.
The frog area is trickier, because the check guage distance between the frog wing rails and the guard rails is critical to keep the wheels from picking the frog point. If the check guage is too wide, filing the inside of the guard rail might help -- or simply moving the guard rail is possible but could be a lot of work. If the check guage is too narrow, then gluing a styrene or metal shim on the inside of the rail head with superglue is an option.
Using a micrometer is essential to getting these dimensions to be spot-on. You want the check guage in HO to be 0.605 exactly.
In a well built turnout, the track guage through the points area is at max track guage (0.672), and the track guage through the frog area is at minimum (0.649) to keep the wheels guided through the frog with minimal wandering. If the track guage doesn't meet these guidelines on the commercial turnout, there's just not much you can do. Tearing the rails out of the plastic ties to move them just isn't an option. Laying your own turnout as has been mentioned is the only real way to get this optimum track guage.
ELECTRICAL ISSUES
With the advent of DCC, having a turnout that's electrically optimum has become a hot topic. In fact, it's got it's own term: DCC friendly, which I discuss here.
Esentially, you want the ability to use either a powered frog or an unpowered frog (with an unpowered frog being easiest), and you want the points to each be the same electrical polarity as their stock rails. For this to work, each point needs to be electrically isolated from the other.
There are other things you can do to ensure the best electrical continuity through a turnout. First, the closure rails need to be directly wired to the stock rails and not depend on getting power through the points. The best option for getting power to the points is to have a turnout that uses continuous points that are all one-piece with the closure rails -- but I don't know of any commercial turnouts that do this.
Baring the contiuous points, then I recommend soldering some fine jumpers between the closure rails and the points to make sure the points get power. Relying on the contact between the points and the stock rails, or the contact between the points and the closure rails to always be reliable is asking for trouble.
FINAL COMMENTS
You can only do so much to improve a commercial turnout and not all reliability issues can be addressed easily. If you want to solve all the issues with commercial turnouts, you will quickly discover building your own turnouts is less work. IMO, using the Central Valley turnout tie strips and the Fast Tracks point and frog jigs makes hand laying a turnout about as goof-proof and affordable as it gets. And I find it's less work than trying to really fix a commercial turnout's issues.
If you insist on using commercial turnouts, I would recommend the Peco Code 83 line. These are some of the best looking turnouts available, they are DCC friendly, and they are some of the best turnouts as to being in guage. I recommend the insulfrog for DCC, although you may need to alter the frog area slightly to avoid shorts as described here.
Joe Fugate
Modeling the 1980s SP Siskiyou Line in southern Oregon